That leaves users of Google's Chrome browser exposed to warnings when they attempt to visit sites certified by CNNIC.
Google claims that CNNIC and a firm called MCS Holdings had been found to have issued "unauthorised digital certificates for several Google domains.
"The decision that Google has made is unacceptable and unintelligible to CNNIC, and meanwhile CNNIC sincerely urge that Google would take users’ rights and interests into full consideration," CNNIC said.
"For the users that CNNIC has already issued the certificates to, we guarantee that your lawful rights and interests will not be affected."
Google withdrew from China in 2010 over censorship issues, and the two have continued to have a problematic relationship, with Beijing moving last year to fully block Google's hugely popular Gmail service.